webchem v1.3.0

NEW FEATURES

• The nist_ri function now returns a column with the CAS number to facilitate querying of multiple retention index tables.
• The nist_ri function can now take multiple arguments for type, polarity and temp_prog.
• CAS numbers are automatically reformatted using as.cas in bcpc_query, cts_convert, get_etoxid, fn_percept, get_cid, and srs_query.
• The as.cas function now has a verbose argument.

DEFUNCT FUNCTIONS

• ci_query() has been removed from the package because NLM had retired ChemIDplus.
• pan_query() has been removed from the package because PAN no longer supports programmatic access.

BUG FIXES

• nist_ri() failed because the behaviour of a dependency had changed. This has been fixed.
• pc_sect() failed when query response was valid but the content was NA. This has been fixed.

webchem v1.2.0

NEW FEATURES

• webchem can now access ChEMBL (https://www.ebi.ac.uk/chembl/) with chembl_*() functions. ChEMBL is a manually curated database of bioactive molecules with drug-like properties.

BUG FIXES

• ChemSpider functions did not include time delays between queries. This has been fixed.
• Multiple ChemSpider functions failed when the API key was provided during function call. This has been fixed.
• Minor change in NIST retention index tables was causing nist_ri() to fail. This has been fixed.

webchem v1.1.3

NEW FEATURES

• cir_query() now returns a tibble instead of a list to be consistent with other translator functions. This is a potentially breaking change for users.

BUG FIXES

• cts_convert() now accepts numeric input as well e.g. PubChem CID.
• get_cid() became more robust to smiles queries with special characters.
• bcpc_query() now correctly parses the activity in cases that two activities are given (e.g. "herbicides" and "plant growth regulators").

webchem v1.1.2

NEW FEATURES

• Export chemical structures in Mol format with write_mol().

BUG FIXES

• ci_query() can no longer query chemicals by name.
• Non-exported function ping_pubchem_pw() was incorrectly reporting that PUG VIEW was down. This has been fixed.
• is.cas() now catches whitespaces correctly.
• aw_query() was renamed and adapted to bcpc_query, as the alanwood site has moved

MINOR IMPROVEMENTS

• webchem functions now default to global options regarding verbose messages.

webchem v1.1.1

NEW FEATURES

• Fetch LIPID MAPS and SwissLipids identifiers from Wikidata.

BUG FIXES

• Fix get_csid() so it doesn't break when a query is invalid.

webchem v1.1.0

NEW FEATURES

• Download images of substances from Chemical Identifier Resolver (CIR) with cir_img().
• Download images of substances from ChemSpider with cs_img().
• find_db() checks if a query gets a hit in most databases integrated in webchem. Useful for deciding which of several databases to focus on given a set of chemicals.

MINOR IMPROVEMENTS

• Most functions now use httr::RETRY() to access webservices.
• Verbose messages are now harmonized.
• The "type" argument in ci_query() and aw_query() has been changed to "from" for consistency with other functions.
• fn_percept() and cts_compinfo() now have "query" and "from" arguments for consistency with other functions.
• Possible values for "from" have been made more consistent across functions.
• pc_synonyms(), cts_convert(), cir_query() have been changed to use the match argument instead of choices for consistency with other functions.
• get_etoxid() output changed slightly so that the matched chemical name string no longer includes the etoxid in parentheses.
• is.cas() is now vectorized.

BUG FIXES

• Fix URL encoding so SMILES queries don't fail on some special characters.

webchem v1.0.0

NEW FEATURES

• get_cid() now can search by registry IDs (e.g. CAS RN), and can handle more complex requests like searching for similar compounds.
• Retrieve chemical data from PubChem content pages with pc_sect().
• get_etoxid() now can search by CAS, EC, GSBL and RTECS numbers. Added from = argument. [PR #241, added by @andschar]
• nist_ri() now can search by name, InChI, InChIKey, or CAS. The cas argument is deprecated. Use query instead with from = "cas"

MINOR IMPROVEMENTS

• all get_*() functions now output tibbles with a column for the query and a column for the retrieved ID
• changes to arguments in get_*() functions to make them more consistent
• aw_idx.rda is no longer included in the package as a data set. Instead, it is built by build_aw_idx() to tempdir().

BUG FIXES

• nist_ri() returned malformed tables or errored if there was only one entry for a query
• get_csid() now returns all csids when queried from formula
• get_csid() returned an error when query was NA [PR #226, fixed by stitam]
• get_chebiid() and chebi_comp_entity() fixed for invalid queries [PR #225, fixed by stitam]
• get_cid() returned the PubChem ID of sodium when the query was NA [PR #223, fixed by stitam]
• aw_query() returned a list for successful queries, NA for unsuccessful queries [PR #222, fixed by stitam]

webchem v0.5.0

NEW FEATURES

• Retrieve data from ChEBI (https://www.ebi.ac.uk/chebi/) webservice with get_chebiid() and chebi_comp_entity(). ChEBI comprises a rich data base on chemicals with bilogical interest [contributed by @andschar].
• Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri() [PR #154, contributed by @Aariq]
• Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query() [PR #179]
• "first" argument in cts_convert() and cir_query() and "interactive" argument in pc_synonyms() deprecated. Use "choices" instead to return either a list of all results, only the first result, or an interactive menu to choose a result to return. [contributed by @Aariq]
• ChemSpider functions now look for an API token stored in .Renviron or .Rprofile by default so you can keep them hidden more easily.

MINOR IMPROVEMENTS

• as.cas() added.
• removed documentation files for non-exported functions that were only used internally.

BUG FIXES

• cs_prop() failed with duplicated return values [issue #148, reported and fixed by @stanstrup]
• pp_query() failed when compound present, but no properties [issue #151, reported and fixed by @stanstrup]
• ci_query() failed when missing table [issue #196, reported and fixed by @gjgetzinger]
• get_csid() failed because of a major change in the ChemSpider API [issue #149, PR #165, contributed by @stitam]
• multiple functions failed because of a major change in the ChemSpider API [issue #149, contributed by @stitam]
• cir_query() mistook NA for sodium [issue #158, reported and fixed by @Aariq]
• fixed functions that communicate with the ChemSpider API [issue #149, issue #160, fixed by @stitam]
• get_etoxid() printed incorrect results for certain match types [issue #201, fixed by @stitam]

DEPRECATED FUNCTIONS

• cs_extcompinfo() cannot be fixed as there is no equivalent in the new ChemSpider API yet.

DEFUNCT FUNCTIONS

• ppdb_parse() has been removed. webchem no longer offers any support for PPDB.
• pp_query() has been removed. Physprop API is no longer active.

webchem v0. 4

webchem 0.4

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

• extr_num() did not work properly with decimal numbers [issue #136, reported and fixed by @stanstrup]
• cs_prop() failed when epi-suite data was not available [issue #139, reported and fixed by @stanstrup]
• cs_prop() failed with invalid html [issue #138, reported and fixed by @stanstrup]
• cs_prop() gave incorrect answer, if entries were not available [issue #142, reported and fixed by @stanstrup]
• cs_prop() did not parse scientific number correctly [issue #143, reported by @stanstrup, fixed by @Edild]
• is.smiles() failed because of changes in rcdk [PR #140, reported and fixed by @allaway]
• cir_query() failed with identifiers containing spaces (e.g. 'acetic acid') [issue #146, reported by Lars Nielsen]
• several other functions failed with identifiers containing spaces & returned wrong distance.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem v0.2

webchem 0.2

NEW FEATURES

• fn_percept() extracts flavor percepts using CAS numbers from www.flavornet.org. Flavornet is a database of 738 compounds with human-detectible odors. [contributed by @Aariq]

MINOR IMPROVEMENTS

BUG FIXES

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS